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123 changes: 67 additions & 56 deletions docs/source/main.bib
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Expand Up @@ -2,93 +2,93 @@ @book{treloar1949physics
title={The Physics of Rubber Elasticity},
author={Treloar, Leslie Ronald George},
year={1949},
location = {Cambridge, UK},
location={Cambridge, UK},
publisher={Clarendon Press},
url = {https://global.oup.com/academic/product/the-physics-of-rubber-elasticity-9780198570271}
url={https://global.oup.com/academic/product/the-physics-of-rubber-elasticity-9780198570271}
}
@book{rubinstein2003polymer,
title={Polymer Physics},
author={Rubinstein, Michael and Colby, Ralph H},
year={2003},
location = {New York},
location={New York},
publisher={Oxford University Press},
url = {https://global.oup.com/academic/product/polymer-physics-9780198520597}
url={https://global.oup.com/academic/product/polymer-physics-9780198520597}
}
@book{mcq,
title={Statistical Mechanics},
author={McQuarrie, Donald A.},
year={2000},
location = {Mill Valley, CA},
location={Mill Valley, CA},
publisher={University Science Books},
url = {https://uscibooks.aip.org/books/statistical-mechanics/}
url={https://uscibooks.aip.org/books/statistical-mechanics/}
}
@book{zwanzig2001nonequilibrium,
title={Nonequilibrium Statistical Mechanics},
author={Zwanzig, Robert},
year={2001},
location = {New York},
location={New York},
publisher={Oxford University Press},
url = {https://global.oup.com/academic/product/nonequilibrium-statistical-mechanics-9780195140187}
url={https://global.oup.com/academic/product/nonequilibrium-statistical-mechanics-9780195140187}
}
@book{bender2013advanced,
title={Advanced Mathematical Methods for Scientists and Engineers I: Asymptotic Methods and Perturbation Theory},
author={Bender, Carl M and Orszag, Steven A},
year={2013},
location = {New York},
location={New York},
publisher={Springer Science \& Business Media},
doi = {10.1007/978-1-4757-3069-2}
doi={10.1007/978-1-4757-3069-2}
}
@book{bleistein1975asymptotic,
title={Asymptotic Expansions of Integrals},
author={Bleistein, Norman and Handelsman, Richard A},
year={1975},
location = {New York},
location={New York},
publisher={Ardent Media},
url={https://store.doverpublications.com/0486650820.html}
}
@article{buche2022freely,
title = {Freely jointed chain models with extensible links},
author = {Buche, Michael R. and Silberstein, Meredith N. and Grutzik, Scott J.},
journal = {Physical Review E},
shortjournal = {Phys. Rev. E},
volume = {106},
pages = {024502},
number = {024502},
numpages = {10},
year = {2022},
publisher = {American Physical Society},
doi = {10.1103/PhysRevE.106.024502},
title={Freely jointed chain models with extensible links},
author={Buche, Michael R. and Silberstein, Meredith N. and Grutzik, Scott J.},
journal={Physical Review E},
shortjournal={Phys. Rev. E},
volume={106},
pages={024502},
number={024502},
numpages={10},
year={2022},
publisher={American Physical Society},
doi={10.1103/PhysRevE.106.024502},
}
@article{buche2020statistical,
title = {Statistical mechanical constitutive theory of polymer networks: The inextricable links between distribution, behavior, and ensemble},
author = {Buche, Michael R. and Silberstein, Meredith N.},
journal = {Physical Review E},
shortjournal = {Phys. Rev. E},
volume = {102},
pages = {012501},
number = {012501},
numpages = {14},
year = {2020},
publisher = {American Physical Society},
doi = {10.1103/PhysRevE.102.012501},
title={Statistical mechanical constitutive theory of polymer networks: The inextricable links between distribution, behavior, and ensemble},
author={Buche, Michael R. and Silberstein, Meredith N.},
journal={Physical Review E},
shortjournal={Phys. Rev. E},
volume={102},
pages={012501},
number={012501},
numpages={14},
year={2020},
publisher={American Physical Society},
doi={10.1103/PhysRevE.102.012501},
}
@article{buche2021chain,
title = {Chain breaking in the statistical mechanical constitutive theory of polymer networks},
journal = {Journal of the Mechanics and Physics of Solids},
volume = {156},
pages = {104593},
year = {2021},
issn = {0022-5096},
doi = {10.1016/j.jmps.2021.104593},
author = {Michael R. Buche and Meredith N. Silberstein},
title={Chain breaking in the statistical mechanical constitutive theory of polymer networks},
journal={Journal of the Mechanics and Physics of Solids},
volume={156},
pages={104593},
year={2021},
issn={0022-5096},
doi={10.1016/j.jmps.2021.104593},
author={Michael R. Buche and Meredith N. Silberstein},
}
@phdthesis{buche2021fundamental,
Expand All @@ -115,27 +115,38 @@ @article{fiasconaro2019analytical
title={Analytical results of the extensible freely jointed chain model},
author={Fiasconaro, Alessandro and Falo, Fernando},
journal={Physica A: Statistical Mechanics and its Applications},
shortjournal = {Physica A},
shortjournal={Physica A},
volume={532},
pages={121929},
year={2019},
publisher={Elsevier},
doi = {10.1016/j.physa.2019.121929}
doi={10.1016/j.physa.2019.121929}
}
@article{radiom2017influence,
title = {Influence of ligand-receptor interactions on force-extension behavior within the freely jointed chain model},
author = {Radiom, Milad and Borkovec, Michal},
journal = {Physical Review E},
shortjournal = {Phys. Rev. E},
volume = {96},
issue = {6},
pages = {062501},
numpages = {7},
year = {2017},
month = {Dec},
publisher = {American Physical Society},
doi = {10.1103/PhysRevE.96.062501}
title={Influence of ligand-receptor interactions on force-extension behavior within the freely jointed chain model},
author={Radiom, Milad and Borkovec, Michal},
journal={Physical Review E},
shortjournal={Phys. Rev. E},
volume={96},
issue={6},
pages={062501},
numpages={7},
year={2017},
month={Dec},
publisher={American Physical Society},
doi={10.1103/PhysRevE.96.062501}
}
@article{becker2010radial,
title={The radial distribution function of worm-like chains},
author={Becker, NB and Rosa, A and Everaers, R},
journal={The European Physical Journal E},
volume={32},
pages={53--69},
year={2010},
publisher={Springer},
doi={10.1140/epje/i2010-10596-0}
}
@article{morse1929diatomic,
Expand All @@ -148,7 +159,7 @@ @article{morse1929diatomic
pages={57},
year={1929},
publisher={APS},
doi = {10.1103/PhysRev.34.57}
doi={10.1103/PhysRev.34.57}
}
@article{jones1924determinationii,
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2 changes: 1 addition & 1 deletion docs/source/physics/single_chain/wlc.rst
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Expand Up @@ -6,7 +6,7 @@ WLC model

Thermodynamics <wlc/thermodynamics>

.. autoclass:: polymers.physics.single_chain.fjc::WLC(number_of_links, link_length, hinge_mass, persistance_length)
.. autoclass:: polymers.physics.single_chain.wlc::WLC(number_of_links, link_length, hinge_mass, persistance_length)

.. autoattribute:: number_of_links
.. autoattribute:: link_length
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2 changes: 1 addition & 1 deletion docs/source/physics/single_chain/wlc/thermodynamics.rst
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Expand Up @@ -5,7 +5,7 @@ WLC model thermodynamics
:maxdepth: 1

Isometric <thermodynamics/isometric>
Isometric <thermodynamics/isotensional>
Isotensional <thermodynamics/isotensional>

.. autoclass:: polymers.physics.single_chain.wlc.thermodynamics::WLC(number_of_links, link_length, hinge_mass, persistance_length)

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Expand Up @@ -25,10 +25,3 @@ WLC model thermodynamics (isotensional)
.. automethod:: nondimensional_gibbs_free_energy_per_link(nondimensional_force, temperature)
.. automethod:: nondimensional_relative_gibbs_free_energy(nondimensional_force)
.. automethod:: nondimensional_relative_gibbs_free_energy_per_link(nondimensional_force)

.. raw::
html
<hr>
.. footbibliography::
4 changes: 3 additions & 1 deletion src/physics/single_chain/wlc/thermodynamics/isometric/mod.jl
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Expand Up @@ -601,9 +601,11 @@ The equilibrium probability density of end-to-end lengths ``g_\\mathrm{eq}`` as
parameterized by the number of links ``N_b``, link length ``\\ell_b``, and persistance length ``\\ell_p``,
```math
g_\\mathrm{eq}(\\xi) = 4\\pi\\xi^2 P_\\mathrm{eq}(\\xi).
g_\\mathrm{eq}(\\xi) = 4\\pi\\xi^2 P_\\mathrm{eq}(\\xi),
```
which is calculated using the accurate analytic approximation provided by [Becker, Rosa, and Everaers](https://doi.org/10.1140/epje/i2010-10596-0).
$(TYPEDSIGNATURES)
"""
function equilibrium_radial_distribution(
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6 changes: 4 additions & 2 deletions src/physics/single_chain/wlc/thermodynamics/isometric/py.rs
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Expand Up @@ -240,10 +240,12 @@ impl WLC
{
nondimensional_end_to_end_length_per_link.as_array().mapv(|nondimensional_end_to_end_length_per_link: f64| super::nondimensional_equilibrium_distribution(&self.nondimensional_persistance_length, &self.normalization_nondimensional_equilibrium_distribution, &nondimensional_end_to_end_length_per_link)).into_pyarray(py)
}
/// The equilibrium probability density of end-to-end lengths as a function of the end-to-end length, given by :footcite:t:`treloar1949physics` as
/// The equilibrium probability density of end-to-end lengths as a function of the end-to-end length,
///
/// .. math::
/// g_\mathrm{eq}(\xi) = 4\pi\xi^2 P_\mathrm{eq}(\xi).
/// g_\mathrm{eq}(\xi) = 4\pi\xi^2 P_\mathrm{eq}(\xi),
///
/// which is calculated using the accurate analytic approximation provided by :footcite:t:`becker2010radial`.
///
/// Args:
/// end_to_end_length (numpy.ndarray): The end-to-end length :math:`\xi`.
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